Gene mapping, describes the methods used to identify the locus of a gene and the distances between genes.[1]

The essence of all genome mapping is to place a collection of molecular markers onto their respective positions on the genome. Molecular markers come in all forms. Genes can be viewed as one special type of genetic markers in the construction of genome maps, and mapped the same way as any other markers.

There are two distinctive types of "Maps" used in the field of genome mapping: genetic maps and physical maps. While both maps are a collection of genetic markers and gene loci, genetic maps' distances are based on the genetic linkage information measured in centimorgans (CM), while physical maps use actual physical distances usually measured in number of base pairs. While the physical map could be a more "accurate" representation of the genome, genetic maps often offer insights into the nature of different regions of the chromosome, e.g. the genetic distance to physical distance ratio varies greatly at different genomic regions which reflects different recombination rates, and such rate is often indicative of euchromatic (usually gene-rich) vs heterochromatic (usually gene poor) regions of the genome.

Researchers begin a genetic map by collecting samples of blood or tissue from family members that carry a prominent disease or trait and family members that don't. Scientists then isolate DNA from the samples and closely examine it, looking for unique patterns in the DNA of the family members who do carry the disease that the DNA of those who don't carry the DNA don't have. These unique molecular patterns in the DNA are referred to as polymorphisms, or markers.[2]

The first steps of building a genetic map are the development of genetic markers and a mapping population. Since the closer the two markers are on the chromosome, the more likely they are to be passed on to the next generation together, therefore the "co-segregation" patterns of all markers can be used to reconstruct their order. With this in mind, the genotypes of each genetic marker are recorded for both parents, and in each individual in the following generations. The quality of the genetic maps is largely dependent upon these two factors: the number of genetic markers on the map and the size of the mapping population. The two factors are interlinked, as a larger mapping population could increase the "resolution" of the map and prevent the map being "saturated".

In genetic mapping, any sequence feature that can be faithfully distinguished from the two parents can be used as a genetic marker. Genes, in this regard, are represented by "traits" that can be faithfully distinguished between two parents. Their linkage with other genetic markers are calculated same way as if they are common markers and the actual gene loci are then bracketed in a region between the two nearest neighbouring markers. This process are then repeated by looking at more markers that target that region to map the gene neighbourhood to a higher resolution until the a specific causative locus can be identified. This process is often referred to as "positional cloning", and used extensively in the study of plant species.

Since actual base-pair distances are generally hard or impossible to directly measure, physical maps are actually constructed by first shattering the genome into hierarchically smaller pieces. By characterizing each single piece and assembling back together, the overlapping path or "tiling path" of these small fragments would allow researchers to infer physical distances between genomic features. The fragmentation of the genome can be achieved by restriction enzyme cutting or by physically shattering the genome by processes like sonication. Once cut, the DNA fragments are separated by electrophoresis. The resulting pattern of DNA migration (i.e. its genetic fingerprint) is used to identify what stretch of DNA is in the clone. By analyzing the fingerprints, contigs are assembled by automated (FPC) or manual means (Pathfinders) into overlapping DNA stretches. Now a good choice of clones can be made to efficiently sequence the clones to determine the DNA sequence of the organism under study.

In physical mapping, there are no direct ways of marking up a specific gene since the mapping do not include any information that concern traits and functions. Genetic markers can be linked to a physical map by processes like in situ hybridization. By this approach, physical map contigs can be "anchored" onto a genetic map. The clones used in the physical map contigs can then be sequenced local scale to help new genetic marker design and identification of the causative loci.

Macrorestriction is a type of physical mapping wherein the high molecular weight DNA is digested with a restriction enzyme having a low number of restriction sites.

There are alternative ways to determine how DNA in a group of clones overlaps without completely sequencing the clones. Once the map is determined, the clones can be used as a resource to efficiently contain large stretches of the genome. This type of mapping is more accurate than genetic maps.

Genome sequencing is sometimes mistakenly referred to as "genome mapping" by non-biologists. The process of "shotgun sequencing" resembles the process of physical mapping: it shatter the genome into small fragments, characterize(sequence) each fragment, and put them back together (more recent sequencing technologies are drastically different). While the scope, purpose and process are totally different, a genome assembly can be viewed as the "ultimate" form of physical map, in that it provides all information that a traditional physical map can offer in a much better way.

Identification of genes is usually the first step in understanding a genome of a species; mapping of the gene is usually the first step of identification of the gene. Gene mapping is usually the starting point of many important downstream studies.

The process to identify a genetic element that is responsible for a disease is also referred to as "mapping". If the locus in which the search is performed is already considerably constrained, the search is called the "fine-mapping" of a gene. This information is derived from the investigation of disease-manifestations in large families (Genetic linkage) or from populations-based genetic association studies.